I still haven't read the full paper and I am busy today and will probably be crashed for the next several days, though I am testing something that might get me through it OK. However:
HERVs are our own genes. They used to be retroviral invaders, but the retroviruses invaded the DNA and became part of us. So this is NOT a viral infection in the normal sense, though there is some speculation that certain viruses might allow HERV genes to become active in combination with new viruses, though I read this stuff a while back.
The main issue seems to be whether the gene becomes active. If its switched on, it can produce viral proteins, just as the cell can produce beneficial proteins. These proteins might provoke an immune response, and hence might lead to autoimmunity.
Normal autoimmune processes to eliminate self-responses might not be valid, because these genes are inactive during immune cell (particularly B cell) development, and so cannot provoke a self response. Its only after these genes are woken up, and become active, that the B cells can respond, and autoimmunity might develop.
Viral infections are suspected of being able to trigger HERV activation. Its not a topic I have looked at a lot recently, so my information is bound to be incomplete and perhaps even wrong. I might need to do some reading on this.
HERVs are contraversial. If it could be demonstrated that a HERV has resurrected and become infectious that would make waves in medical science. I think some are trying to do that. However it seems to me that dysregulation of HERV genes leading to viral protein synthesis might be enough.
This may induce local tissue inflammation. We know that most of the latent pathogens suspected in ME, and infecting B cells, become reactivated and infect inflammed tissue. That is the link with existing latent infections.
HERVs could also affect immune function. This will alter our reponse to new pathogens.
This research is far from giving conclusive useful results, but its very interesting and perhaps deserves some deep consideration.